I deleted some files on the source and ran the Mirror (Update) function from a USB drive to a portable hard drive. It deleted all the files and subdirectories except this one.
"R:\PortableApps Backup\Documents\M3 DS Real\NDS-GBM-GBA Movie Converter 1.20 (Crystal Engine)"
That is the full path but the target folder is just R:\PortableApps Backup. It deleted all the other sudbirectories and files under 'M3 DS Real' except that one. Is the total path to long or the paraenthesis causing an issue?
I did run it a second time and it completely skips over it with no change on the destination.
Thank you and also thank you for a great program... 
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I tried to reproduce the error to no avail. I am pretty anal with running scandisk and defrag so I know I had no corruption on the source or destination but for whatever reason I am unable to reproduce the error. The changes were significant is the only thing I can think (as in several hundred files on a 4GB USB drive). Anyway I still think it's some sort of glitch but it seems to be working. Thanks for the help.
I was sure that I had replied to your post stating that I couldn't reproduce and recommending that you tried again with version 2 when it is released as it uses a different method of working out exclusions. As it is I'm glad it's working for you now.